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alignment.check_sequence_structure() -- check sequence/structure alignment for sanity

check_sequence_structure(gapdist=8.0, io=None)
This command checks the alignment of the target sequence (the last entry in the alignment) with each of the templates: For all consecutive pairs of $ {C}_\alpha$ atoms in the target, it calculates the distance between the two equivalent $ {C}_\alpha$ atoms in each of the templates. If the distance is longer than gapdist Å, it is reported. In such a case, the alignment between the template and the target is almost certainly incorrect. The total number of exceeded pair distances is returned.

Ben Webb 2008-05-05